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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ), 'gf_id' => 'HOM05D001152', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001152' ), 'data_identifier' => 'HOM05D001152', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001152', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35530' => 'bna', 'A03p67980' => 'bna', 'A05p40360' => 'bna', 'A08p33030' => 'bna', 'A09p64110' => 'bna', 'Aa31LG1G2650' => 'aar', 'Aa31LG2G150' => 'aar', 'Aa31LG5G18430' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1891' => 'aag', 'Actinidia00108' => 'ach', 'Actinidia05052' => 'ach', 'Actinidia07893' => 'ach', 'Actinidia09528' => 'ach', 'Actinidia09768' => 'ach', 'Actinidia10781' => 'ach', 'Actinidia11886' => 'ach', 'Actinidia13721' => 'ach', 'Actinidia13722' => 'ach', 'Actinidia27740' => 'ach', 'Ah.01g001750' => 'amhyb', 'Ah.06g181590' => 'amhyb', 'Ah.13g077700' => 'amhyb', 'Ah.14g082920' => 'amhyb', 'Ah.14g087630' => 'amhyb', 'AL1G23330' => 'aly', 'AL2G13420' => 'aly', 'Aqoxy1G02952' => 'aox', 'Aqoxy2G03711' => 'aox', 'arahy.Tifrunner.gnm1.ann1.24SSM1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3N9Z1Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5QP4QH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.734IZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQ90Z3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ES3V94' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GKC2FH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMG1BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PR438B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRFK83' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RD3CQX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE4FFN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5W2QE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZS4L0E' => 'arhy', 'AT1G12070' => 'ath', 'AT1G62450' => 'ath', 'AT3G07880' => 'ath', 'ATR0686G042' => 'atr', 'ATR0712G055' => 'atr', 'ATR0736G046' => 'atr', 'Atru.chr1.2447' => 'acertr', 'Atru.chr5.1782' => 'acertr', 'Atru.chr5.1785' => 'acertr', 'Atru.chr6.3327' => 'acertr', 'AUR62008762' => 'cqu', 'AUR62012796' => 'cqu', 'AUR62015092' => 'cqu', 'AUR62015920' => 'cqu', 'AUR62017550' => 'cqu', 'AUR62018505' => 'cqu', 'AUR62020914' => 'cqu', 'AUR62021858' => 'cqu', 'AUR62024752' => 'cqu', 'AUR62025475' => 'cqu', 'BcaB02g06426' => 'bca', 'BcaB02g11333' => 'bca', 'BcaB03g13212' => 'bca', 'BcaB04g21267' => 'bca', 'BcaB07g31328' => 'bca', 'BcaB08g37431' => 'bca', 'BcaC02g10448' => 'bca', 'BcaC04g22400' => 'bca', 'BcaC04g22766' => 'bca', 'BcaC05g25223' => 'bca', 'BcaC05g29578' => 'bca', 'BcaC06g31902' => 'bca', 'BcaC07g41732' => 'bca', 'BcaC07g41733' => 'bca', 'BcaC07g41749' => 'bca', 'BcaC09g47955' => 'bca', 'BcaC09g47959' => 'bca', 'BcaC09g47962' => 'bca', 'BolC1t05521H' => 'bol', 'BolC3t16586H' => 'bol', 'BolC5t29853H' => 'bol', 'BolC5t34601H' => 'bol', 'BolC8t49148H' => 'bol', 'BolC8t52310H' => 'bol', 'BolC9t54459H' => 'bol', 'BolC9t54878H' => 'bol', 'BraA01t02674Z' => 'bra', 'BraA01t04355Z' => 'bra', 'BraA03t12728Z' => 'bra', 'BraA06t24127Z' => 'bra', 'BraA08t35223Z' => 'bra', 'BraA09t36956Z' => 'bra', 'BraA09t37263Z' => 'bra', 'BraA09t41757Z' => 'bra', 'C03p43170' => 'bna', 'C04p28800' => 'bna', 'C05p59450' => 'bna', 'C08p15180' => 'bna', 'C08p47710' => 'bna', 'C09p19760' => 'bna', 'CAN.G1186.40' => 'can', 'CAN.G1263.15' => 'can', 'CAN.G3639.1' => 'can', 'CAN.G449.19' => 'can', 'CAN.G767.2' => 'can', 'CANSAT01G2258' => 'cansat', 'CANSAT56G2595' => 'cansat', 'CANSAT64G2605' => 'cansat', 'CANSAT78G1308' => 'cansat', 'CARHR012440' => 'chi', 'CARHR049430' => 'chi', 'CARHR082610' => 'chi', 'CARHR181550' => 'chi', 'Carub.0001s1176' => 'cru', 'Carub.0002s0251' => 'cru', 'Carub.0003s0746' => 'cru', 'Ca_00721_v3' => 'car', 'Ca_08692_v3' => 'car', 'Ca_16353_v3' => 'car', 'Ca_16441_v3' => 'car', 'Ca_18014_v3' => 'car', 'Ca_21045_v3' => 'car', 'CBR_g50391' => 'cbr', 'Cc00_g20940' => 'ccan', 'Cc01_g18020' => 'ccan', 'Cc03_g10010' => 'ccan', 'Cc09_g00860' => 'ccan', 'CDE02G2138' => 'cde', 'CDE04G0241' => 'cde', 'CDE07G0796' => 'cde', 'CDE09G1337' => 'cde', 'Cfa000105' => 'cfa', 'Cfa002463' => 'cfa', 'Cfa008684' => 'cfa', 'Cfa012838' => 'cfa', 'Ciclev10016372m.g' => 'ccl', 'Ciclev10016457m.g' => 'ccl', 'Ciclev10021950m.g' => 'ccl', 'CiPaw.01G110100' => 'cil', 'CiPaw.02G061500' => 'cil', 'CiPaw.03G268300' => 'cil', 'CiPaw.03G276300' => 'cil', 'CiPaw.09G102400' => 'cil', 'CiPaw.10G078000' => 'cil', 'ClCG01G010200' => 'cla', 'ClCG01G021490' => 'cla', 'ClCG02G002510' => 'cla', 'ClCG02G002550' => 'cla', 'ClCG07G001240' => 'cla', 'ClCG07G015500' => 'cla', 'COL.COLO4_08687' => 'col', 'COL.COLO4_31608' => 'col', 'COL.COLO4_31886' => 'col', 'COL.COLO4_36580' => 'col', 'Cpa.g.sc136.1' => 'cpa', 'Cpa.g.sc165.40' => 'cpa', 'Cpa.g.sc75.115' => 'cpa', 'Cpa.g.sc987.4' => 'cpa', 'CsaV3_1G004930' => 'csa', 'CsaV3_1G017230' => 'csa', 'CsaV3_3G028170' => 'csa', 'CsaV3_4G003120' => 'csa', 'CsaV3_6G048510' => 'csa', 'CsaV3_7G002870' => 'csa', 'CSS0000106' => 'camsi', 'CSS0001486' => 'camsi', 'CSS0010316' => 'camsi', 'CSS0010515' => 'camsi', 'CSS0035397' => 'camsi', 'CSS0043903' => 'camsi', 'CSS0046691' => 'camsi', 'DCAR_012568' => 'dca', 'DCAR_013204' => 'dca', 'DCAR_016642' => 'dca', 'DCAR_021116' => 'dca', 'DCAR_027822' => 'dca', 'DCAR_030872' => 'dca', 'DCAR_032167' => 'dca', 'Dinv05851' => 'din', 'Dinv07404' => 'din', 'Dinv07833' => 'din', 'Dinv13680' => 'din', 'Dinv13967' => 'din', 'Dinv16377' => 'din', 'Dinv22219' => 'din', 'Dinv34656' => 'din', 'Dinv40818' => 'din', 'Duzib133G0407' => 'dzi', 'Duzib133G0804' => 'dzi', 'Duzib138G0435' => 'dzi', 'Duzib138G0717' => 'dzi', 'Duzib138G0911' => 'dzi', 'Duzib151G0827' => 'dzi', 'Duzib160G0791' => 'dzi', 'Duzib192G0169' => 'dzi', 'Duzib211G0309' => 'dzi', 'Duzib235G0566' => 'dzi', 'Duzib268G0182' => 'dzi', 'ECA233G1260' => 'eca', 'ECA236G2933' => 'eca', 'ECA240G3733' => 'eca', 'ECA240G4287' => 'eca', 'EL10Ac3g05655' => 'bvu', 'EL10Ac3g05895' => 'bvu', 'EL10Ac3g07410' => 'bvu', 'EL10Ac4g07639' => 'bvu', 'EL10Ac4g10099' => 'bvu', 'EL10Ac7g17646' => 'bvu', 'EL10Ac8g20191' => 'bvu', 'Eucgr.D01404' => 'egr', 'Eucgr.D01410' => 'egr', 'Eucgr.E03927' => 'egr', 'Eucgr.H00495' => 'egr', 'Eucgr.L02974' => 'egr', 'Eucgr.L03554' => 'egr', 'FAN02G1347' => 'fan', 'FAN05G0613' => 'fan', 'FAN07G2122' => 'fan', 'FAN09G2607' => 'fan', 'FAN12G2151' => 'fan', 'FAN14G3067' => 'fan', 'FAN15G1455' => 'fan', 'FAN17G1810' => 'fan', 'FAN20G0500' => 'fan', 'FAN21G2547' => 'fan', 'FAN22G2193' => 'fan', 'FAN24G2014' => 'fan', 'FAN25G3592' => 'fan', 'FAN27G0509' => 'fan', 'FvH4_2g20900' => 'fve', 'FvH4_3g00970' => 'fve', 'FvH4_4g12520' => 'fve', 'FvH4_6g41510' => 'fve', 'Glyma.02G307600' => 'gma', 'Glyma.05G149100' => 'gma', 'Glyma.07G265200' => 'gma', 'Glyma.08G105700' => 'gma', 'Glyma.09G010300' => 'gma', 'Glyma.10G039300' => 'gma', 'Glyma.11G252600' => 'gma', 'Glyma.13G125700' => 'gma', 'Glyma.14G005400' => 'gma', 'Glyma.15G114800' => 'gma', 'Glyma.17G008800' => 'gma', 'Glyma.18G004300' => 'gma', 'Glyma.19G166700' => 'gma', 'Gohir.A02G015700' => 'ghi', 'Gohir.A05G174700' => 'ghi', 'Gohir.A07G086400' => 'ghi', 'Gohir.A07G189500' => 'ghi', 'Gohir.A08G049600' => 'ghi', 'Gohir.A09G208900' => 'ghi', 'Gohir.A11G132400' => 'ghi', 'Gohir.D02G017100' => 'ghi', 'Gohir.D05G177600' => 'ghi', 'Gohir.D07G091500' => 'ghi', 'Gohir.D07G195600' => 'ghi', 'Gohir.D08G059700' => 'ghi', 'Gohir.D09G202350' => 'ghi', 'Gohir.D11G138500' => 'ghi', 'Gorai.001G098000' => 'gra', 'Gorai.001G219100' => 'gra', 'Gorai.004G061600' => 'gra', 'Gorai.005G021000' => 'gra', 'Gorai.006G226200' => 'gra', 'Gorai.007G148600' => 'gra', 'Gorai.009G183100' => 'gra', 'GSVIVG01003335001' => 'vvi', 'GSVIVG01028385001' => 'vvi', 'GSVIVG01030419001' => 'vvi', 'GSVIVG01031620001' => 'vvi', 'HanXRQChr02g0033101' => 'han', 'HanXRQChr02g0034831' => 'han', 'HanXRQChr02g0038541' => 'han', 'HanXRQChr03g0076931' => 'han', 'HanXRQChr04g0111291' => 'han', 'HanXRQChr08g0233191' => 'han', 'HanXRQChr17g0535411' => 'han', 'HanXRQChr17g0557271' => 'han', 'Haze_06181' => 'cav', 'Haze_06921' => 'cav', 'Haze_08660' => 'cav', 'Haze_11703' => 'cav', 'Haze_12722' => 'cav', 'Haze_13476' => 'cav', 'Haze_24670' => 'cav', 'Haze_24675' => 'cav', 'Hma1.2p1_0036F.1_g022980' => 'hma', 'Hma1.2p1_0619F.1_g190410' => 'hma', 'Hma1.2p1_0657F.1_g197160' => 'hma', 'Hma1.2p1_1112F.1_g258520' => 'hma', 'HPP92_021400' => 'vpl', 'Hund05469' => 'sun', 'Hund19033' => 'sun', 'Hund21153' => 'sun', 'Hund24450' => 'sun', 'Lalb_Chr04g0247171' => 'lal', 'Lalb_Chr06g0170631' => 'lal', 'Lalb_Chr07g0176991' => 'lal', 'Lalb_Chr15g0087991' => 'lal', 'Lalb_Chr18g0056951' => 'lal', 'Lalb_Chr20g0119271' => 'lal', 'Lalb_Chr23g0278221' => 'lal', 'Lj1A1240T34' => 'lonja', 'Lj1C71G9' => 'lonja', 'Lj1g0012272' => 'lja', 'Lj1g0026779' => 'lja', 'Lj2C261T2' => 'lonja', 'Lj2g0001523' => 'lja', 'Lj4g0007350' => 'lja', 'Lj4g0021199' => 'lja', 'Lj4g0023326' => 'lja', 'Lj6g0009204' => 'lja', 'Lj8A132T61' => 'lonja', 'LjContig00081g0003637' => 'lja', 'Lsat_1_v5_gn_4_1800' => 'lsa', 'Lsat_1_v5_gn_7_113480' => 'lsa', 'Lsat_1_v5_gn_7_95621' => 'lsa', 'Lsat_1_v5_gn_8_28541' => 'lsa', 'Lsat_1_v5_gn_8_92261' => 'lsa', 'Lsat_1_v5_gn_9_105441' => 'lsa', 'Lsat_1_v5_gn_9_41241' => 'lsa', 'Lsat_1_v5_gn_9_91001' => 'lsa', 'Manes.05G194201' => 'mes', 'Manes.08G071200' => 'mes', 'Manes.09G076319' => 'mes', 'Manes.12G035100' => 'mes', 'Manes.12G060400' => 'mes', 'Manes.13G037600' => 'mes', 'Manes.13G063901' => 'mes', 'Mapoly0021s0134' => 'mpo', 'Mapoly0029s0034' => 'mpo', 'MBI07_g40035_MAGBIO' => 'mbi', 'MBI10_g19234_MAGBIO' => 'mbi', 'MBI19_g06146_MAGBIO' => 'mbi', 'MD04G1025800' => 'mdo', 'MD05G1192500' => 'mdo', 'MD05G1357900' => 'mdo', 'MD09G1119200' => 'mdo', 'MD10G1179000' => 'mdo', 'MD10G1331800' => 'mdo', 'MD17G1110100' => 'mdo', 'Medtr2g025740' => 'mtr', 'Medtr3g082970' => 'mtr', 'Medtr3g084940' => 'mtr', 'Medtr4g133060' => 'mtr', 'Medtr7g097270' => 'mtr', 'Medtr8g097200' => 'mtr', 'MELO3C007434.2' => 'cme', 'MELO3C012863.2' => 'cme', 'MELO3C017734.2' => 'cme', 'MELO3C018889.2' => 'cme', 'MELO3C021683.2' => 'cme', 'Migut.H01783' => 'egut', 'Migut.M01396' => 'egut', 'Migut.N02219' => 'egut', 'MSTRG.13117' => 'ama', 'MSTRG.14613' => 'ama', 'MSTRG.15779' => 'ama', 'MSTRG.16028' => 'ama', 'MSTRG.17506' => 'ama', 'Nitab4.5_0000143g0190' => 'nta', 'Nitab4.5_0001109g0030' => 'nta', 'Nitab4.5_0001735g0100' => 'nta', 'Nitab4.5_0002389g0130' => 'nta', 'Nitab4.5_0003295g0100' => 'nta', 'Nitab4.5_0003785g0030' => 'nta', 'Nitab4.5_0004406g0040' => 'nta', 'Nitab4.5_0004758g0010' => 'nta', 'Nitab4.5_0007541g0050' => 'nta', 'Nitab4.5_0023224g0010' => 'nta', 'Nn1g02842' => 'nnu', 'Nn1g03308' => 'nnu', 'Nn1g07390' => 'nnu', 'Nn1g08278' => 'nnu', 'Nn3g19732' => 'nnu', 'Nn7g37656' => 'nnu', 'Oeu007167.1' => 'oeu', 'Oeu009389.1' => 'oeu', 'Oeu016821.1' => 'oeu', 'Oeu016825.1' => 'oeu', 'Oeu019627.1' => 'oeu', 'Oeu035713.1' => 'oeu', 'Oeu050343.1' => 'oeu', 'Os01g0913600' => 'osa', 'Os02g0719000' => 'osa', 'Os06g0318300' => 'osa', 'Peaxi162Scf00352g00213' => 'pax', 'Peaxi162Scf00378g00512' => 'pax', 'Peaxi162Scf00415g00312' => 'pax', 'Peaxi162Scf00442g00413' => 'pax', 'Peaxi162Scf00610g00014' => 'pax', 'PGR004G1700' => 'pgr', 'PGR042G1435' => 'pgr', 'PGR042G3022' => 'pgr', 'PGR142G3795' => 'pgr', 'PGSC0003DMG400008461' => 'stu', 'PGSC0003DMG400013348' => 'stu', 'PGSC0003DMG400023558' => 'stu', 'PGSC0003DMG401004581' => 'stu', 'Phvul.001G163100' => 'pvu', 'Phvul.001G263700' => 'pvu', 'Phvul.003G083600' => 'pvu', 'Phvul.006G143100' => 'pvu', 'Phvul.008G287600' => 'pvu', 'Phvul.L003646' => 'pvu', 'Potri.002G223200' => 'ptr', 'Potri.002G234600' => 'ptr', 'Potri.002G259200' => 'ptr', 'Potri.006G010500' => 'ptr', 'Potri.014G163000' => 'ptr', 'Potri.016G013700' => 'ptr', 'Pp3c10_19650' => 'ppa', 'Pp3c10_19740' => 'ppa', 'Pp3c22_3980' => 'ppa', 'Pp3c3_32980' => 'ppa', 'Pp3c3_33010' => 'ppa', 'Prupe.1G175100' => 'ppe', 'Prupe.3G205000' => 'ppe', 'Prupe.4G010300' => 'ppe', 'Prupe.8G218800' => 'ppe', 'Psat1g176080' => 'psa', 'Psat3g055840' => 'psa', 'Psat4g005160' => 'psa', 'Psat5g103800' => 'psa', 'Psat7g076600' => 'psa', 'PSO017G4698' => 'pso', 'PSO210G4648' => 'pso', 'PSO541G1404' => 'pso', 'PSO675G8327' => 'pso', 'PSO675G8712' => 'pso', 'PSO761G0341' => 'pso', 'QL05p015046' => 'qlo', 'QL05p069690' => 'qlo', 'QL06p027969' => 'qlo', 'QL08p029498' => 'qlo', 'QL09p040533' => 'qlo', 'RcHm_v2.0_Chr2g0157191' => 'rch', 'RcHm_v2.0_Chr4g0411301' => 'rch', 'RcHm_v2.0_Chr4g0411311' => 'rch', 'RcHm_v2.0_Chr4g0411341' => 'rch', 'RcHm_v2.0_Chr5g0001491' => 'rch', 'RcHm_v2.0_Chr6g0287301' => 'rch', 'Rhsim01G0261500' => 'rsi', 'Rhsim02G0099200' => 'rsi', 'Rhsim06G0171300' => 'rsi', 'Rhsim06G0225000' => 'rsi', 'Rhsim06G0225100' => 'rsi', 'Sabra02G0170300' => 'sbr', 'Sabra02G0179000' => 'sbr', 'Sabra06G0008600' => 'sbr', 'Sabra14G0124400' => 'sbr', 'Sabra16G0001900' => 'sbr', 'Sabra16G0016100' => 'sbr', 'SalBow6G0995' => 'sbo', 'SalBow8G1334' => 'sbo', 'SalBow8G3646' => 'sbo', 'Sc03g0008180' => 'sci', 'Sc13g0000590' => 'sci', 'Sc17g0007750' => 'sci', 'Sc19g0007530' => 'sci', 'Sc21g0000980' => 'sci', 'Sed0002551' => 'sed', 'Sed0007700' => 'sed', 'Sed0011070' => 'sed', 'Sed0013769' => 'sed', 'Sed0018367' => 'sed', 'Sed0019304' => 'sed', 'Sed0020362' => 'sed', 'SEGI_17836' => 'sgi', 'SEGI_32603' => 'sgi', 'SGA_v2.0_scaffold17G08046' => 'sas', 'SGA_v2.0_scaffold42G16184' => 'sas', 'SGA_v2.0_scaffold478G52223' => 'sas', 'SGA_v2.0_scaffold49G18243' => 'sas', 'SGA_v2.0_scaffold4G01875' => 'sas', 'SMO270G0002' => 'smo', 'SMO361G0557' => 'smo', 'Solyc04g014760.3' => 'sly', 'Solyc05g054110.3' => 'sly', 'Solyc09g072670.3' => 'sly', 'Solyc11g012270.2' => 'sly', 'Solyc12g098650.2' => 'sly', 'Sopen04g006870' => 'spe', 'Sopen05g032600' => 'spe', 'Sopen09g028480' => 'spe', 'Sopen11g007050' => 'spe', 'Sp1g10750' => 'spa', 'Sp2g02150' => 'spa', 'Sp3g06800' => 'spa', 'TAR362G0729' => 'tar', 'TAR362G1139' => 'tar', 'TAR624G0389' => 'tar', 'TAR626G0161' => 'tar', 'TAR627G0350' => 'tar', 'TAR627G0818' => 'tar', 'THA.LOC104809470' => 'tha', 'THA.LOC104809866' => 'tha', 'THA.LOC104819051' => 'tha', 'THA.LOC104826662' => 'tha', 'Thecc.01G185900' => 'tca', 'Thecc.01G253400' => 'tca', 'Thecc.04G188300' => 'tca', 'Thecc.06G233500' => 'tca', 'Thhalv10009559m.g' => 'esa', 'Thhalv10021395m.g' => 'esa', 'Thhalv10023681m.g' => 'esa', 'TPR.G13066' => 'tpr', 'TPR.G22465' => 'tpr', 'TPR.G26568' => 'tpr', 'TPR.G37076' => 'tpr', 'TPR.G9202' => 'tpr', 'TWI12G0629' => 'twi', 'TWI36G1649' => 'twi', 'TWI38G0607' => 'twi', 'TWI38G2211' => 'twi', 'TWI63G1307' => 'twi', 'unitig_32.g11052' => 'ugi', 'unitig_37.g12190' => 'ugi', 'unitig_748.g7917' => 'ugi', 'vmacro11575' => 'vma', 'vmacro12134' => 'vma', 'vmacro14808' => 'vma', 'vmacro15760' => 'vma', 'VMungo0251G0401' => 'vmu', 'VMungo0540G0844' => 'vmu', 'VMungo0647G0163' => 'vmu', 'VMungo1215G1846' => 'vmu', 'VMungo1383G2902' => 'vmu', 'VMungo1383G3627' => 'vmu', 'Zm00001eb189390' => 'zma', 'Zm00001eb252880' => 'zma', 'Zm00001eb286700' => 'zma', 'Zm00001eb350260' => 'zma', 'Zm00001eb350270' => 'zma' ) $gf_id = 'HOM05D001152' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001152' ) $data_identifier = 'HOM05D001152' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 14, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 8, 'lsa' => (int) 8, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb350270' $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